Dev master sync (#274)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Release/2.9.1 (#205)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Dev version bump (#202)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Attribute mapping from node to dug element (#203)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* adding more config options for node extraction

* some refactoring

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Changed DbGaP to SPARC in the scicrunch parser (#204)

* Release/2.9.1

Renames SPARC datasets as SPARC instead of dbgap

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>
Co-authored-by: Howard Lander <[email protected]>

* Update _version.py (#206)

* Release/2.9.2 (#209)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Dev version bump (#202)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Attribute mapping from node to dug element (#203)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* adding more config options for node extraction

* some refactoring

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Changed DbGaP to SPARC in the scicrunch parser (#204)

* Anvil (#207)

* Added updated anvil dataset catalog

* Added script for downloading all anvil data dicts

* Added current anvil data dictionaries to data folder to be used for indexing

* Anvil parser (#208)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* anvil parser

* bump number of files test

* Update dbgap_parser.py

* Update anvil_dbgap_parser.py

change to AnVIL

* Update test_parsers.py

update test

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>
Co-authored-by: Howard Lander <[email protected]>
Co-authored-by: Alex Waldrop <[email protected]>

* Release 2.9.3 (#244)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Dev version bump (#202)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Attribute mapping from node to dug element (#203)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* adding more config options for node extraction

* some refactoring

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Changed DbGaP to SPARC in the scicrunch parser (#204)

* Anvil (#207)

* Added updated anvil dataset catalog

* Added script for downloading all anvil data dicts

* Added current anvil data dictionaries to data folder to be used for indexing

* Anvil parser (#208)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* anvil parser

* bump number of files test

* Update dbgap_parser.py

* Update anvil_dbgap_parser.py

change to AnVIL

* Update test_parsers.py

update test

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Initial Kaniko build.

* Move version file definition.

* Quote env vars.

* Update env vars.

* Update env vars.

* Update env vars.

* env var changes.

* env var changes.

* env var changes.

* env var changes.

* Update DOCKER_IMAGE var.

* Update DOCKER_IMAGE var in kaniko cmd.

* Update kaniko destination line.

* Update kaniko destination line.

* Moree variable madness.

* Programatically remove quotes from version tag.

* dug dump concepts api created and tested (#229)

Co-authored-by: Nathan Braswell <[email protected]>

* Update _version.py (#234)

* Version changes + separate build and publish.

* Semantic versioning prep.

* Add develop and master versioning and tagging.

* Ncpi index fix (#232)

* Renamed anvil to ncpi

* Update ncpi datasets catalog

* Modified script to download NCPI datasets into platform subfolders

* Updated NCPI integration dataset

* Removed unused variable

* Removed ncpi top level folder to spread results among subfolders

* Change output dir to data instead of ncpi subdir

* Moved NCPI subdirs into main data folder for ingest as per Yaphet's request

Co-authored-by: Alex Waldrop <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>
Co-authored-by: Howard Lander <[email protected]>
Co-authored-by: Alex Waldrop <[email protected]>
Co-authored-by: Charles Bennett <[email protected]>
Co-authored-by: Nathaniel Braswell <[email protected]>
Co-authored-by: Nathan Braswell <[email protected]>
Co-authored-by: cnbennett3 <[email protected]>
Co-authored-by: Alex Waldrop <[email protected]>

* Release/2.9.4 (#260)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Dev version bump (#202)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Attribute mapping from node to dug element (#203)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* adding more config options for node extraction

* some refactoring

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Changed DbGaP to SPARC in the scicrunch parser (#204)

* Anvil (#207)

* Added updated anvil dataset catalog

* Added script for downloading all anvil data dicts

* Added current anvil data dictionaries to data folder to be used for indexing

* Anvil parser (#208)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* anvil parser

* bump number of files test

* Update dbgap_parser.py

* Update anvil_dbgap_parser.py

change to AnVIL

* Update test_parsers.py

update test

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Initial Kaniko build.

* Move version file definition.

* Quote env vars.

* Update env vars.

* Update env vars.

* Update env vars.

* env var changes.

* env var changes.

* env var changes.

* env var changes.

* Update DOCKER_IMAGE var.

* Update DOCKER_IMAGE var in kaniko cmd.

* Update kaniko destination line.

* Update kaniko destination line.

* Moree variable madness.

* Programatically remove quotes from version tag.

* dug dump concepts api created and tested (#229)

Co-authored-by: Nathan Braswell <[email protected]>

* Update _version.py (#234)

* Version changes + separate build and publish.

* Semantic versioning prep.

* Add develop and master versioning and tagging.

* Bump version.

* Revert version to dug format.

* Ncpi index fix (#232)

* Renamed anvil to ncpi

* Update ncpi datasets catalog

* Modified script to download NCPI datasets into platform subfolders

* Updated NCPI integration dataset

* Removed unused variable

* Removed ncpi top level folder to spread results among subfolders

* Change output dir to data instead of ncpi subdir

* Moved NCPI subdirs into main data folder for ingest as per Yaphet's request

Co-authored-by: Alex Waldrop <[email protected]>

* Add github creds env var.

* Fix version typo.

* Initial commit

* Reduce ephemeral storage limits and requests

* More parsers (#248)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* consolidate dbgap format parser in single file , adds crdc and kfdrc parsers

* adding tests

* bump version

* parser when versions of studies are > 9

* test for version

* fix long text issues, and encoding errors

* nltk initialization

* change nltk approach for sliding window

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* update version

* remove cruft from merge

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>
Co-authored-by: Howard Lander <[email protected]>
Co-authored-by: Alex Waldrop <[email protected]>
Co-authored-by: Charles Bennett <[email protected]>
Co-authored-by: Nathaniel Braswell <[email protected]>
Co-authored-by: Nathan Braswell <[email protected]>
Co-authored-by: cnbennett3 <[email protected]>
Co-authored-by: Alex Waldrop <[email protected]>
Co-authored-by: Hoid <[email protected]>

* Release/2.9.5 (#266)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Dev version bump (#202)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Attribute mapping from node to dug element (#203)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* adding more config options for node extraction

* some refactoring

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Changed DbGaP to SPARC in the scicrunch parser (#204)

* Anvil (#207)

* Added updated anvil dataset catalog

* Added script for downloading all anvil data dicts

* Added current anvil data dictionaries to data folder to be used for indexing

* Anvil parser (#208)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* anvil parser

* bump number of files test

* Update dbgap_parser.py

* Update anvil_dbgap_parser.py

change to AnVIL

* Update test_parsers.py

update test

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Initial Kaniko build.

* Move version file definition.

* Quote env vars.

* Update env vars.

* Update env vars.

* Update env vars.

* env var changes.

* env var changes.

* env var changes.

* env var changes.

* Update DOCKER_IMAGE var.

* Update DOCKER_IMAGE var in kaniko cmd.

* Update kaniko destination line.

* Update kaniko destination line.

* Moree variable madness.

* Programatically remove quotes from version tag.

* dug dump concepts api created and tested (#229)

Co-authored-by: Nathan Braswell <[email protected]>

* Update _version.py (#234)

* Version changes + separate build and publish.

* Semantic versioning prep.

* Add develop and master versioning and tagging.

* Bump version.

* Revert version to dug format.

* Ncpi index fix (#232)

* Renamed anvil to ncpi

* Update ncpi datasets catalog

* Modified script to download NCPI datasets into platform subfolders

* Updated NCPI integration dataset

* Removed unused variable

* Removed ncpi top level folder to spread results among subfolders

* Change output dir to data instead of ncpi subdir

* Moved NCPI subdirs into main data folder for ingest as per Yaphet's request

Co-authored-by: Alex Waldrop <[email protected]>

* Add github creds env var.

* Fix version typo.

* Initial commit

* Reduce ephemeral storage limits and requests

* More parsers (#248)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* consolidate dbgap format parser in single file , adds crdc and kfdrc parsers

* adding tests

* bump version

* parser when versions of studies are > 9

* test for version

* fix long text issues, and encoding errors

* nltk initialization

* change nltk approach for sliding window

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Master to develop sync (#262)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Release/2.9.1 (#205)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Dev version bump (#202)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Attribute mapping from node to dug element (#203)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* adding more config options for node extraction

* some refactoring

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Changed DbGaP to SPARC in the scicrunch parser (#204)

* Release/2.9.1

Renames SPARC datasets as SPARC instead of dbgap

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>
Co-authored-by: Howard Lander <[email protected]>

* Update _version.py (#206)

* Release/2.9.2 (#209)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Dev version bump (#202)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Attribute mapping from node to dug element (#203)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* adding more config options for node extraction

* some refactoring

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Changed DbGaP to SPARC in the scicrunch parser (#204)

* Anvil (#207)

* Added updated anvil dataset catalog

* Added script for downloading all anvil data dicts

* Added current anvil data dictionaries to data folder to be used for indexing

* Anvil parser (#208)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* anvil parser

* bump number of files test

* Update dbgap_parser.py

* Update anvil_dbgap_parser.py

change to AnVIL

* Update test_parsers.py

update test

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>
Co-authored-by: Howard Lander <[email protected]>
Co-authored-by: Alex Waldrop <[email protected]>

* Release 2.9.3 (#244)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Dev version bump (#202)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Attribute mapping from node to dug element (#203)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* adding more config options for node extraction

* some refactoring

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Changed DbGaP to SPARC in the scicrunch parser (#204)

* Anvil (#207)

* Added updated anvil dataset catalog

* Added script for downloading all anvil data dicts

* Added current anvil data dictionaries to data folder to be used for indexing

* Anvil parser (#208)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* anvil parser

* bump number of files test

* Update dbgap_parser.py

* Update anvil_dbgap_parser.py

change to AnVIL

* Update test_parsers.py

update test

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Initial Kaniko build.

* Move version file definition.

* Quote env vars.

* Update env vars.

* Update env vars.

* Update env vars.

* env var changes.

* env var changes.

* env var changes.

* env var changes.

* Update DOCKER_IMAGE var.

* Update DOCKER_IMAGE var in kaniko cmd.

* Update kaniko destination line.

* Update kaniko destination line.

* Moree variable madness.

* Programatically remove quotes from version tag.

* dug dump concepts api created and tested (#229)

Co-authored-by: Nathan Braswell <[email protected]>

* Update _version.py (#234)

* Version changes + separate build and publish.

* Semantic versioning prep.

* Add develop and master versioning and tagging.

* Ncpi index fix (#232)

* Renamed anvil to ncpi

* Update ncpi datasets catalog

* Modified script to download NCPI datasets into platform subfolders

* Updated NCPI integration dataset

* Removed unused variable

* Removed ncpi top level folder to spread results among subfolders

* Change output dir to data instead of ncpi subdir

* Moved NCPI subdirs into main data folder for ingest as per Yaphet's request

Co-authored-by: Alex Waldrop <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>
Co-authored-by: Howard Lander <[email protected]>
Co-authored-by: Alex Waldrop <[email protected]>
Co-authored-by: Charles Bennett <[email protected]>
Co-authored-by: Nathaniel Braswell <[email protected]>
Co-authored-by: Nathan Braswell <[email protected]>
Co-authored-by: cnbennett3 <[email protected]>
Co-authored-by: Alex Waldrop <[email protected]>

* Release/2.9.4 (#260)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Dev version bump (#202)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Attribute mapping from node to dug element (#203)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* adding more config options for node extraction

* some refactoring

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Changed DbGaP to SPARC in the scicrunch parser (#204)

* Anvil (#207)

* Added updated anvil dataset catalog

* Added script for downloading all anvil data dicts

* Added current anvil data dictionaries to data folder to be used for indexing

* Anvil parser (#208)

* Release/2.8.0 (#198)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* Release/v2.9.0 (#201)

* Bumping version

* support for extracting dug elements from graph (#197)

* support for extracting dug elements from graph

* adding flag for enabling dug element extraction from graph

* adding new config for node_to dug element parsing

* adding more parameters to crawler to able configuration to element extraction logic

* add tests

* add tests for crawler

Co-authored-by: Yaphetkg <[email protected]>

* Display es scores (#199)

* Include ES scores in variable results

* Round ES score to 6

* Update _version.py (#200)

* Update _version.py

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* anvil parser

* bump number of files test

* Update dbgap_parser.py

* Update anvil_dbgap_parser.py

change to AnVIL

* Update test_parsers.py

update test

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* Initial Kaniko build.

* Move version file definition.

* Quote env vars.

* Update env vars.

* Update env vars.

* Update env vars.

* env var changes.

* env var changes.

* env var changes.

* env var changes.

* Update DOCKER_IMAGE var.

* Update DOCKER_IMAGE var in kaniko cmd.

* Update kaniko destination line.

* Update kaniko destination line.

* Moree variable madness.

…

src/dug/core/parsers/bacpac_parser.py

@@ -9,7 +9,7 @@
 
 
 class BACPACParser(FileParser):
-    # Class for parsers SPRINT Data dictionary into a set of Dug Elements
+    # Class for parsing BACPAC data dictionaries in dbGaP XML format into a set of Dug Elements.
 
     @staticmethod
     def parse_study_name_from_filename(filename: str):